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Yeah, the test epub is a bit of a mess structurally, but it is valid, so Sigil should be able to handle it. But it doesn't. The files are being moved to Sigil's mandated structure OK, but the files' entries in the opf manifest whose hrefs start with the relative "../" are not being updated to the their new locations during Sigil's normal Source Updates. Will have to check into that.
As a workaround in the meantime, using the "Tools->Arrange into folders" feature of calibre's editor (on any epubs you edited with calibre) to make sure files are arranged into Text/, Styles, Images/, Fonts/ folders (OPF and NCX fields empty) will ensure that Sigil will be able to open the epub and successfully update the links. You must, of course, save the epub after making those changes in calibre's editor.
Thanks for pointing out the problem.
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